This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project represents a number of different ways that were tested to better identify transcription factors (TFs) in nuclear protein samples. In this study, a peptide inclusion list was created that contained a large number of peptides corresponding to TFs. Although the inclusion list was overly large, the results oddly showed an increase in the number of TFs identified. I am still not entirely sure why this method worked better than the standard DDA approach, but have set up future experiments to better understand this. My current hypothesis is that I may be able to replicate these results by just doing a DDA experiment where I tell the instrument to ignore the top 2 highest abundant peaks.